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pilF

ID: 1513898156 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 566 (548)
Sequences: 3933 (2677.1)
Seq/Len: 7.177
Nf(neff/√len): 114.4

HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied

Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 7.177).

Sequences per length for each position, AFTER the coverage/gap filter was applied
Legend: If visible, the positions blocked in grey are regions that have > 75% gaps and were automatically trimmed and excluded in the GREMLIN analysis.

Trim query Generate MSA using: Filter MSA GREMLIN
Start: End: E-value: Iterations: Coverage: Remove gaps: Prior:

GREMLIN Results:
Residue pairs sorted by coevolution strength:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.

ij Scaled score Prob
514_T537_E5.0361.00
458_L491_P4.5671.00
464_K492_V4.4641.00
520_I533_Q4.0121.00
311_Y339_G3.8431.00
283_K349_N3.7511.00
463_K489_Y3.6281.00
465_E487_K3.5901.00
237_S284_I3.3731.00
424_S427_E3.3311.00
84_E88_R3.2391.00
314_A448_L3.2251.00
461_H496_N3.1721.00
312_L342_I3.0921.00
458_L556_S3.0311.00
351_S384_F3.0221.00
131_V136_L2.9591.00
105_G131_V2.8341.00
520_I525_G2.8271.00
325_T420_L2.8221.00
253_K373_Q2.7691.00
279_L357_V2.7571.00
348_I391_V2.7101.00
457_K505_V2.7021.00
513_N521_I2.6731.00
313_A512_K2.6311.00
464_K490_S2.5961.00
535_R544_T2.5921.00
267_K290_D2.5871.00
315_L339_G2.5581.00
466_H488_L2.5491.00
546_G560_V2.4821.00
545_S549_K2.4271.00
188_V236_I2.4221.00
459_C497_C2.4071.00
458_L463_K2.3901.00
276_L367_V2.3671.00
353_A380_A2.3411.00
21_D24_T2.3201.00
283_K365_N2.2941.00
212_Y233_A2.2931.00
424_S531_A2.2921.00
271_F286_M2.2921.00
517_L530_I2.2531.00
514_T533_Q2.2521.00
275_T284_I2.2491.00
397_I406_A2.2431.00
519_R523_E2.2191.00
308_K312_L2.2101.00
450_I510_V2.1921.00
505_V554_I2.1871.00
516_A537_E2.1831.00
466_H490_S2.1681.00
429_L446_V2.1641.00
469_P472_T2.1531.00
533_Q537_E2.0671.00
199_G502_K2.0331.00
511_V539_F2.0151.00
343_L391_V2.0081.00
22_E26_R1.9861.00
274_N387_Q1.9411.00
426_A511_V1.9311.00
543_R564_T1.9241.00
224_E227_K1.9001.00
323_L418_S1.8811.00
306_D540_N1.8631.00
491_P556_S1.8611.00
95_L129_L1.8591.00
462_C494_C1.8531.00
221_M562_R1.8341.00
106_L128_A1.8321.00
244_A273_V1.8291.00
533_Q536_K1.8171.00
59_A66_Y1.8161.00
370_N373_Q1.8131.00
488_L550_A1.8091.00
305_E309_E1.8051.00
458_L489_Y1.8041.00
246_L275_T1.8011.00
17_N60_E1.7891.00
529_E532_E1.7831.00
344_N350_I1.7781.00
271_F288_I1.7691.00
132_E135_K1.7671.00
278_T365_N1.7631.00
459_C462_C1.7621.00
526_N529_E1.7601.00
426_A530_I1.7441.00
547_L551_M1.7271.00
317_Q447_N1.7171.00
459_C494_C1.7121.00
50_Q53_A1.7001.00
211_T227_K1.6931.00
465_E489_Y1.6841.00
343_L417_M1.6581.00
501_Y555_T1.6551.00
460_S463_K1.6541.00
404_E408_K1.6211.00
304_E307_Q1.6151.00
462_C497_C1.6121.00
494_C497_C1.6121.00
307_Q508_Y1.6011.00
458_L492_V1.5951.00
523_E529_E1.5951.00
322_I415_M1.5931.00
367_V384_F1.5921.00
540_N548_L1.5851.00
261_M271_F1.5841.00
289_L359_I1.5781.00
403_A437_V1.5751.00
309_E313_A1.5741.00
28_A43_L1.5681.00
221_M456_R1.5661.00
376_D379_Q1.5611.00
9_G12_K1.5611.00
507_I546_G1.5481.00
550_A560_V1.5471.00
274_N285_V1.5000.99
380_A384_F1.4990.99
307_Q510_V1.4990.99
462_C493_G1.4890.99
468_V488_L1.4870.99
548_L552_Q1.4820.99
466_H472_T1.4780.99
224_E346_T1.4750.99
525_G529_E1.4730.99
461_H502_K1.4680.99
306_D310_L1.4630.99
240_L273_V1.4630.99
8_S16_L1.4570.99
303_Y508_Y1.4520.99
68_D135_K1.4460.99
283_K351_S1.4350.99
397_I418_S1.4280.99
535_R541_D1.4260.99
303_Y311_Y1.4230.99
549_K554_I1.4220.99
307_Q310_L1.4220.99
378_S401_E1.4210.99
37_Q45_Q1.4120.99
515_P518_Q1.3990.99
516_A536_K1.3890.99
516_A533_Q1.3740.99
196_I269_I1.3730.99
108_D111_N1.3660.99
86_L90_H1.3650.99
103_F129_L1.3610.98
259_I271_F1.3450.98
213_R224_E1.3420.98
353_A384_F1.3320.98
534_A538_G1.3250.98
118_I126_T1.3230.98
8_S12_K1.3120.98
101_K127_E1.3070.98
95_L105_G1.3050.98
534_A539_F1.3030.98
91_R107_S1.2920.98
433_L442_L1.2890.98
353_A369_V1.2860.98
88_R141_E1.2840.98
244_A259_I1.2810.98
59_A64_I1.2780.97
316_K342_I1.2720.97
303_Y335_S1.2670.97
555_T559_E1.2640.97
11_A25_A1.2570.97
91_R137_G1.2480.97
411_Q441_N1.2470.97
501_Y556_S1.2460.97
297_G300_A1.2450.97
67_C131_V1.2430.97
243_M259_I1.2400.97
505_V549_K1.2390.97
455_A555_T1.2370.97
426_A531_A1.2290.97
442_L446_V1.2220.96
218_T223_H1.2180.96
400_L436_G1.2130.96
82_I87_V1.2090.96
221_M347_D1.2080.96
310_L512_K1.2070.96
51_S134_D1.2020.96
183_P186_R1.1990.96
541_D544_T1.1950.96
13_Q61_Q1.1900.96
468_V473_L1.1860.96
10_L61_Q1.1830.96
133_D137_G1.1820.95
206_E215_R1.1820.95
507_I563_V1.1820.95
28_A42_H1.1780.95
493_G497_C1.1710.95
91_R133_D1.1670.95
470_K474_L1.1610.95
532_E536_K1.1490.95
490_S558_E1.1480.94
429_L521_I1.1470.94
307_Q545_S1.1460.94
205_F212_Y1.1410.94
322_I448_L1.1400.94
304_E552_Q1.1400.94
87_V140_I1.1350.94
68_D71_S1.1340.94
507_I564_T1.1320.94
345_T348_I1.1270.94
547_L550_A1.1270.94
446_V449_I1.1260.94
384_F392_I1.1250.94
269_I290_D1.1250.94
20_L25_A1.1220.94
307_Q450_I1.1210.94
428_T449_I1.1200.93
199_G218_T1.1130.93
94_P97_K1.1120.93
407_I437_V1.1100.93
392_I409_A1.1090.93
314_A447_N1.1080.93
253_K375_M1.0990.93
314_A510_V1.0950.92
105_G136_L1.0940.92
323_L397_I1.0910.92
49_V54_L1.0850.92
336_L393_M1.0840.92
367_V375_M1.0800.92
11_A61_Q1.0790.92
191_M214_V1.0780.92
303_Y506_G1.0760.92
185_V239_R1.0760.92
299_D312_L1.0760.92
200_S218_T1.0760.92
321_M416_V1.0750.92
53_A56_E1.0750.92
374_G379_Q1.0670.91
105_G129_L1.0660.91
194_D198_G1.0640.91
29_Q40_V1.0610.91
451_A542_L1.0560.91
82_I94_P1.0520.90
93_L136_L1.0500.90
426_A527_S1.0500.90
344_N363_G1.0440.90
191_M203_L1.0420.90
459_C493_G1.0360.89
551_M554_I1.0270.89
299_D308_K1.0250.89
304_E548_L1.0250.89
472_T475_H1.0240.89
107_S131_V1.0090.88
262_R268_S1.0020.87
11_A40_V1.0010.87
Legend: Only predictions with Scaled Score > 1 are listed. For all 3L/2 predictions, click on one of the links below.
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
NEW Features
HHsearch Results: (06Aug15)
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
PDB M Cov P(%) HHΔ  
4phtA30.77561000.348Contact Map
4ksrA301000.424Contact Map
1p9rA10.66611000.444Contact Map
2ewvA10.56891000.612Contact Map
3jvvA30.56361000.621Contact Map
2oap120.79151000.68Contact Map
2eyuA20.3941000.722Contact Map
4ihqA30.80921000.726Contact Map
4bloA120.47531000.73Contact Map
2b8tA40.33041000.811Contact Map
M = number of chains, if homo-oligomer
Cov = coverage of hit
P(%) = probability

Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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